MIC (version 1.1.0)

pull_PATRIC_genomes: Automated download of genomes from PATRIC database

Description

Automated download of genomes from PATRIC database

Usage

pull_PATRIC_genomes(
  output_directory,
  taxonomic_name = NULL,
  database = patric_ftp_path,
  filter = "MIC",
  ab = NULL,
  n_genomes = 0
)

Value

The number of failed downloads (i.e., 0 if all attempted downloads were successful).

Arguments

output_directory

local directory to save to

taxonomic_name

character of taxonomic bacterial name to download

database

local or ftp path to PATRIC database, or loaded database using load_patric_db()

filter

"MIC" or "disk" or "all" phenotypes

ab

antibiotic(s) of interest, provided as a character vector of antibiotic names/codes, or ideally, as AMR::ab classes, created using AMR::as.ab (default = all)

n_genomes

number of genomes (0 = all)

Examples

# \donttest{
pull_PATRIC_genomes(tempdir(),
                    taxonomic_name = "Escherichia coli",
                    filter = "MIC",
                    n_genomes = 10)
# }